I have always had luck with putting the reference letter right in back of the resume and cover letter. that makes you stand out from the millions of other applicants, and it shows them that you have at least one place that likes you. if they don’t care to see it, then you’ve only wasted a piece of paper. it might be what gets you called vs. the rest.

I would advice that you give your credential only during the interview with your future direct manager. He’s the one really interested in knowing you better.
Managers will choose you because your profile matches what they search for, and then ask confirmation to your reference.
They won’t choose you because your reference told you were a great candidate.
Second, as most of the times you need to apply for 100 postings before finding the right job, you take the risk to overwhelm your reference contacts with phone calls about you. If they’re busy, they won’t be happy to be disturbed, and you’ll lose them.
Third, it’s better to say to your reference, such person will call you for such job where I need such competences. You cannot do that everytime you apply for a job.